Thanks for your instant reply, Justin. Dear all,
Please correct me if I am woring here....but...reading through the user-list, I gathered that -vis option og g_energy oes not give good results and instead cos_accleration should be used from the following reference. >@Article{Hess2002b, > author = {B. Hess}, > title = {Determining the shear viscosity of model liquids from >molecular simulation}, > journal = {J. Chem. Phys.}, > year = 2002, > volume = 116, > pages = {209-217} >} I am trying to get the results of viscosity through cos_acceleration that probably are formatted as below (taken from a user-list). > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------------------------- > 1/Viscosity ( s/kg) Thanks again, SN --- On Sat, 4/16/11, Justin A. Lemkul <jalem...@vt.edu> wrote: From: Justin A. Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] 1/viscosity from g_energy To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Saturday, April 16, 2011, 3:06 PM shikha nangia wrote: > Dear gmx-users, > > I am trying to obtain 1/viscosity values for my system after using the > cos_acceleration option in the mdp file. My gromacs version is 4.5.4 released > on March 21, 2011. > When I try using the g_energy option for my file > > g_energy -f ener.edr -o outfile.xvg > > I get the following options > > End your selection with an empty line or a zero. > ------------------------------------------------------------------- > 1 Bond 2 Angle 3 Improper-Dih. 4 LJ-(SR) > 5 Disper.-corr. 6 Coulomb-(SR) 7 Potential 8 Kinetic-En. > 9 Total-Energy 10 Conserved-En. 11 Temperature 12 Pres.-DC >13 Pressure 14 Box-XX 15 Box-YY 16 Box-ZZ >17 Box-YX 18 Box-ZX 19 Box-ZY 20 Volume >21 Density 22 pV 23 Enthalpy 24 Vir-XX >25 Vir-XY 26 Vir-XZ 27 Vir-YX 28 Vir-YY >29 Vir-YZ 30 Vir-ZX 31 Vir-ZY 32 Vir-ZZ >33 Pres-XX 34 Pres-XY 35 Pres-XZ 36 Pres-YX >37 Pres-YY 38 Pres-YZ 39 Pres-ZX 40 Pres-ZY 41 Pres-ZZ 42 #Surf*SurfTen 43 Mu-X 44 Mu-Y 45 Mu-Z 46 T-System 47 Lamb-System > > I am not sure which option (1 to 47) gives 1/viscosity. I tried looking > through the manual and searching the user list but could not resolve the > issue. > > Please let me know what am I missing here. > Use -vis rather than -o. -Justin > Thanks, > SN > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists